Man pages for novasmedley/gbmSpm
Find predictive sequential patterns for clinical glioblastoma patients
| aucs | Sets the performance metric to be area under the AUC and PR... |
| cleanData | Clean data to desired format ready for 'arulesSequences'. |
| createEventNames | Create unique event names for each attribute of an event... |
| createTransactions | Convert events into transactions. |
| discretizeKPS | Discretize KPS according to expert opinion |
| discretizeTumVols | Discretize tumor volume. |
| findPatternDays | Find People with a sequence pattern in their events |
| getAge | Calculate numeric age. |
| getAgeDecade | Get age decade. |
| getChemoOverlapEvents | Get events that overlap with chemotherapy, specifically just... |
| getCV | Perform cross-validation on training partition. |
| getData | Get patient event and survival data from a database |
| getFeatureVectors | Create feature vectors that can be used for logit modeling |
| getFit | Fit logit model using cross-validation |
| getLaterality | Parse the tumor location string to get laterality. |
| getLocation | Parse the tumor location string to get location |
| getModelStruct | Get logit coefficients |
| getPatIDs | Get patient IDs. |
| getPerformanceNames | Get colnames that will be kept for averaging across cross... |
| getROC_PR | depends on ROCR |
| getSeqPatterns | Get sequential patterns |
| getTestResults | Apply |
| getTrainingFolds | Create patient-independent folds in cross-validation in... |
| getTrainResults | get training results of fitted model retrained on entire... |
| getTrainTestPartition | Partition patients into testing and training datasets based... |
| getTumorLocation | Get the tumor location and laterality. |
| getTumorNames | Get column names of labels and non-spm features to... |
| getVolTypeName | Get the full name of the tumor volume type. |
| plotMultiROC | Multiple ROC plots in one and also faceted |
| plotROC | Plot multiple performance curves in one graph |
| prepDemographics | Add and prep demographic information (static 'events') to... |
| prepLaterality | Prepare tumor laterality feature for logit modeling. |
| prepLocation | Prepare tumor location feature for logit modeling. |
| prepLogitData | Create data for logit model. |
| prepSurvivalLabels | Prep survival information (labels for all classifictation... |
| prepTumorVol | Get all tumor volume types. |
| removeData | Formats event strings and removes incorrect or missing... |
| removePreRadiation | Remove events which occurred prior to a patient's first... |
| removeVisits | Remove clinical visits with no history of length 'maxgap'. |
| resetEventIDsToDays | Convert event dates into relative days. |
| retrainLogit | Retrain logit after hyperparameter selection. |
| runCV | Run logit modeling |
| runSPM | Run sequential pattern mining |
| selectROCThreshold | Select the roc threshold with the max F1 score and calculate... |
| setContinDiscrete | Discretize tumor volumes into intervals, where each interval... |
| setDataCols | Remove unwanted or keep interested columns from logit data |
| setPercentChange | Calculate different tumor volume information types. |
| vectorizePatterns | Create a binary vector of patterns observed at a clinical... |
